SMTL ID : 7chh.1

Cryo-EM structure of the SARS-CoV-2 S-6P in complex with BD-368-2 Fabs

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 2 residues within 4Å: Chain A: N.717, L.922 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain B: N.717, L.922 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.3: 3 residues within 4Å: Chain B: N.1098, T.1100, H.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain C: N.717, L.922, N.925, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.925

31 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.6: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.122, T.124 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.282 Chain C: K.558 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.343 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.709 Chain C: D.796 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.801, Q.804 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.282 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: A.706, S.711, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: F.342, N.343 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: G.339, N.343 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Du, S. et al., Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy. Cell (2020)

Release Date

2020-09-16

Peptides

Spike glycoprotein: ABC
BD-368-2 Fab heavy chain: DFH
BD-368-2 Fab light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
G

H
J

E
E

G
H

I
K

Spike glycoprotein

BD-368-2 Fab heavy chain

BD-368-2 Fab light chain

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